[Mrtrix-discussion] empty ROI
Manuel Blesa Cábez
mblesac at gmail.com
Wed Jun 4 10:28:15 PDT 2014
Hi Donald,
I checked it for all the ROIs and the values are not 0 and 1. Are 0 outside
the roi and between 0 and 1 in the ROI. Do you think this is the motive?
How can I make it binary?
Regards,
Manuel Blesa
2014-06-04 19:13 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
> Hi Manuel,
>
> OK, I guess the transform wasn't the issue... The only other possibility I
> can think of is that the values in the ROI image aren't the expected 0 & 1.
> Can you load the ROI image in MRView and check that the intensity values
> outside the ROI are zero and those inside the ROI are one?
>
> Cheers,
> Donald
>
> --
> Dr J-Donald Tournier (PhD)
>
> Senior Lecturer, Biomedical Engineering
> Division of Imaging Sciences & Biomedical Engineering
> King's College London
>
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH
> T: +44 (0)20 7188 7118 ext 53613
> W:
> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>
> On 4 Jun 2014 18:06, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>
>> Hi Donald,
>>
>> This is the mrinfo for the fod:
>>
>> ************************************************
>> Image: "fod.mif"
>> ************************************************
>> Format: MRtrix
>> Dimensions: 120 x 110 x 54 x 45
>> Voxel size: 1.4 x 1.4 x 2.8 x 1
>> Data type: 32 bit float (little endian)
>> Data strides: [ 2 3 4 1 ]
>> Intensity scaling: offset = 0, multiplier = 1
>> Comments: FSL5.0
>> Transform: 1 0 0 2.788e+04
>> -0 1 0 -3.487e+04
>> -0 0 1 -5.623e+04
>> 0 0 0 1
>>
>>
>> The rest of the ROIs, have the same mrinfo that the problematic ROI. I
>> check it with both programs, fslview and mrview and with both looks ok.
>>
>> To calculate this ROIs I did it with FSL, because i calculated on the
>> template after do the TBSS, to see differences betwen groups, and after
>> this I did the inverse transform to the subject space. Can some of this
>> steps affect to the transform of the ROI?
>>
>> Regards,
>>
>> Manuel Blesa
>>
>>
>> 2014-06-04 18:54 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
>>
>>> Hi Manuel,
>>>
>>> The translation column of the transform seems way out - about 30 metres
>>> off isocentre... Does the ROI overlay properly onto your fod.mif image
>>> within MRView? Does your fod.mif image have the same translation - what
>>> does mrinfo report for that image? I expect whatever you used to generate
>>> the ROI has corrupted the transform. When you said the ROI looks OK on
>>> visual inspection, was that with fslview or MRView? I think fslview just
>>> overlays images voxel-wise, with no regard for any differences in the
>>> transforms. Basically, if the two images don't overlap in scanner
>>> coordinates, then that would explain your issue...
>>>
>>> Cheers,
>>> Donald
>>>
>>> --
>>> Dr J-Donald Tournier (PhD)
>>>
>>> Senior Lecturer, Biomedical Engineering
>>> Division of Imaging Sciences & Biomedical Engineering
>>> King's College London
>>>
>>> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
>>> Thomas' Hospital, London. SE1 7EH
>>> T: +44 (0)20 7188 7118 ext 53613
>>> W:
>>> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>>>
>>> On 4 Jun 2014 17:39, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>>>
>>>> Hi Donald,
>>>>
>>>> This is the 'mrinfo roi_CC1.mif'
>>>>
>>>> ************************************************
>>>> Image: "roi_CC1.mif"
>>>> ************************************************
>>>> Format: MRtrix
>>>> Dimensions: 120 x 110 x 54
>>>> Voxel size: 1.4 x 1.4 x 2.8
>>>> Data type: 32 bit float (little endian)
>>>> Data strides: [ -1 2 3 ]
>>>> Intensity scaling: offset = 0, multiplier = 1
>>>> Comments: FSL5.0
>>>> Transform: 1 0 0 2.788e+04
>>>> -0 1 0 -3.487e+04
>>>> -0 0 1 -5.623e+04
>>>> 0 0 0 1
>>>>
>>>> Regards,
>>>>
>>>> Manuel Blesa
>>>>
>>>>
>>>> 2014-06-04 18:33 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
>>>>
>>>>> Hi Manuel,
>>>>>
>>>>> Can you post the output of 'mrinfo roi_CC1.mif' ? Would be good to
>>>>> also have some info as to how the image was generated. Hopefully that'll
>>>>> help to narrow down the problem...
>>>>>
>>>>> Cheers,
>>>>> Donald
>>>>>
>>>>> --
>>>>> Dr J-Donald Tournier (PhD)
>>>>>
>>>>> Senior Lecturer, Biomedical Engineering
>>>>> Division of Imaging Sciences & Biomedical Engineering
>>>>> King's College London
>>>>>
>>>>> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
>>>>> Thomas' Hospital, London. SE1 7EH
>>>>> T: +44 (0)20 7188 7118 ext 53613
>>>>> W:
>>>>> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>>>>>
>>>>> On 4 Jun 2014 17:01, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have a strange problem, I'm sure is easy to solve but I'm stuck on
>>>>>> this and I don't find the solution.
>>>>>>
>>>>>> I want to calculate the tracks for a ROI, and when I run it I obtain
>>>>>> the following message:
>>>>>>
>>>>>> tckgen fod.mif tracks_CC1.tck -algorithm SD_STREAM -grad
>>>>>> ag140128a_6_HARDI_WT_ref.b -seed_image roi_CC1.mif -mask mask.mif -number
>>>>>> 1000
>>>>>>
>>>>>> tckgen [ERROR]: Cannot use image roi_CC1.mif as ROI - image is empty
>>>>>>
>>>>>> I opened the ROI and it looks ok, and is not "outside" of the fod
>>>>>> map. I did the same, for another ROI and it works correctly. I don't know
>>>>>> way this ROI has this problem, Somebody can help me? Maybe is due to the
>>>>>> location of the ROI and the default parameters? Thanks in advance.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Manuel Blesa
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mrtrix-discussion mailing list
>>>>>> Mrtrix-discussion at www.nitrc.org
>>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>>
>>>>>>
>>>>
>>
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